Class CodonAdaptationIndex
source code
This class implements the codon adaptaion index (CAI) described by
Sharp and Li (Nucleic Acids Res. 1987 Feb 11;15(3):1281-95).
methods:
set_cai_index(Index):
This mehtod sets-up an index to be used when calculating CAI for a
gene. Just pass a dictionary similar to the SharpEcoliIndex in
CodonUsageIndices module.
generate_index(FastaFile):
This method takes a location of a FastaFile and generates an index.
This index can later be used to calculate CAI of a gene.
cai_for_gene(DNAsequence):
This mehtod uses the Index (either the one you set or the one you
generated) and returns the CAI for the DNA sequence.
print_index(): This method prints out the index you used.